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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ), 'gf_id' => 'HOM05D001466', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001466' ), 'data_identifier' => 'HOM05D001466', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001466', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '432', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26510' => 'bna', 'A01p26520' => 'bna', 'A04p21480' => 'bna', 'A06p05080' => 'bna', 'A06p21570' => 'bna', 'A07p09920' => 'bna', 'A07p18920' => 'bna', 'A08p24430' => 'bna', 'A08p35390' => 'bna', 'A09p36000' => 'bna', 'A09p66070' => 'bna', 'Aa31LG4G14390' => 'aar', 'Aa31LG5G7860' => 'aar', 'Aa31LG6G11720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.895' => 'aag', 'Actinidia03723' => 'ach', 'Actinidia07140' => 'ach', 'Actinidia07141' => 'ach', 'Actinidia24106' => 'ach', 'Actinidia31389' => 'ach', 'Actinidia32366' => 'ach', 'Actinidia32367' => 'ach', 'Ah.01g002990' => 'amhyb', 'Ah.01g014280' => 'amhyb', 'Ah.01g014290' => 'amhyb', 'Ah.14g086160' => 'amhyb', 'AL1G18330' => 'aly', 'AL1G44480' => 'aly', 'AL4G21680' => 'aly', 'AL5G23720' => 'aly', 'Aqoxy1G01230' => 'aox', 'Aqoxy1G01605' => 'aox', 'arahy.Tifrunner.gnm1.ann1.048NTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.581AXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6KD87U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7DE8S1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CRM3FV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZG0NG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M326I4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PW0UPQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQF818' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZNEZ2M' => 'arhy', 'AT1G07990' => 'ath', 'AT1G08005' => 'ath', 'AT1G30470' => 'ath', 'AT2G28360' => 'ath', 'AT3G45190' => 'ath', 'ATR0048G001' => 'atr', 'ATR0165G008' => 'atr', 'Atru.chr10.877' => 'acertr', 'Atru.chr3.3615' => 'acertr', 'AUR62024962' => 'cqu', 'AUR62034028' => 'cqu', 'AUR62038592' => 'cqu', 'AUR62042192' => 'cqu', 'BcaB01g01104' => 'bca', 'BcaB02g06695' => 'bca', 'BcaB03g13358' => 'bca', 'BcaB03g13826' => 'bca', 'BcaB06g28208' => 'bca', 'BcaB07g32654' => 'bca', 'BcaB07g32679' => 'bca', 'BcaB07g32680' => 'bca', 'BcaC01g00194' => 'bca', 'BcaC01g00195' => 'bca', 'BcaC01g01984' => 'bca', 'BcaC02g08183' => 'bca', 'BcaC02g08184' => 'bca', 'BcaC02g08185' => 'bca', 'BcaC05g24716' => 'bca', 'BcaC09g49704' => 'bca', 'BcaNung05262' => 'bca', 'BolC1t03327H' => 'bol', 'BolC3t19242H' => 'bol', 'BolC3t19932H' => 'bol', 'BolC4t23806H' => 'bol', 'BolC4t27272H' => 'bol', 'BolC5t29363H' => 'bol', 'BolC5t31672H' => 'bol', 'BolC7t42016H' => 'bol', 'BolC8t47147H' => 'bol', 'BolC8t52551H' => 'bol', 'BraA01t02581Z' => 'bra', 'BraA01t02582Z' => 'bra', 'BraA04t17714Z' => 'bra', 'BraA06t23714Z' => 'bra', 'BraA06t25244Z' => 'bra', 'BraA07t28781Z' => 'bra', 'BraA08t34398Z' => 'bra', 'BraA08t35445Z' => 'bra', 'BraA09t39123Z' => 'bra', 'BraA09t41945Z' => 'bra', 'C01p33760' => 'bna', 'C03p69820' => 'bna', 'C03p76780' => 'bna', 'C04p23120' => 'bna', 'C04p57510' => 'bna', 'C05p06040' => 'bna', 'C05p29440' => 'bna', 'C07p15120' => 'bna', 'C08p03440' => 'bna', 'C08p50220' => 'bna', 'CAN.G1001.46' => 'can', 'CAN.G312.14' => 'can', 'CAN.G631.33' => 'can', 'CAN.G954.25' => 'can', 'CANSAT54G1935' => 'cansat', 'CARHR007780' => 'chi', 'CARHR029870' => 'chi', 'CARHR121290' => 'chi', 'CARHR121300' => 'chi', 'CARHR150770' => 'chi', 'CARHR150780' => 'chi', 'Carub.0001s0735' => 'cru', 'Carub.0001s2867' => 'cru', 'Carub.0004s0928' => 'cru', 'Carub.0005s1098' => 'cru', 'Ca_00808_v3' => 'car', 'Ca_01406_v3' => 'car', 'Ca_19267_v3' => 'car', 'CBR_g12239' => 'cbr', 'Cc01_g11060' => 'ccan', 'Cc02_g07060' => 'ccan', 'Cc09_g08120' => 'ccan', 'CDE02G0430' => 'cde', 'CDE02G4191' => 'cde', 'CDE04G3573' => 'cde', 'CDE05G0731' => 'cde', 'CDE07G0784' => 'cde', 'Cfa000828' => 'cfa', 'Cfa011310' => 'cfa', 'Cfa027049' => 'cfa', 'Ciclev10014271m.g' => 'ccl', 'Ciclev10027836m.g' => 'ccl', 'CiPaw.09G115800' => 'cil', 'CiPaw.10G086000' => 'cil', 'CiPaw.13G113900' => 'cil', 'CiPaw.14G081400' => 'cil', 'ClCG01G025090' => 'cla', 'ClCG02G021200' => 'cla', 'COL.COLO4_18324' => 'col', 'COL.COLO4_26824' => 'col', 'Cpa.g.c30685' => 'cpa', 'Cpa.g.sc17.92' => 'cpa', 'Cpa.g.sc17.94' => 'cpa', 'Cpa.g.sc17.95' => 'cpa', 'Cpa.g.sc65.1' => 'cpa', 'Cpa.g.sc65.2' => 'cpa', 'Cre12.g484150' => 'cre', 'CsaV3_6G013950' => 'csa', 'CsaV3_6G052290' => 'csa', 'CSS0008518' => 'camsi', 'CSS0026120' => 'camsi', 'CSS0027231' => 'camsi', 'DCAR_003860' => 'dca', 'DCAR_007845' => 'dca', 'Dinv01991' => 'din', 'Dinv03059' => 'din', 'Dinv17921' => 'din', 'Dinv32736' => 'din', 'Duzib160G0813' => 'dzi', 'Duzib168G0088' => 'dzi', 'Duzib235G1003' => 'dzi', 'Duzib235G1512' => 'dzi', 'ECA233G0670' => 'eca', 'ECA234G3392' => 'eca', 'ECA236G0430' => 'eca', 'ECA246G3821' => 'eca', 'ECA248G0050' => 'eca', 'EL10Ac8g19553' => 'bvu', 'EL10Ac9g22531' => 'bvu', 'Eucgr.B02505' => 'egr', 'Eucgr.D00188' => 'egr', 'FAN11G3248' => 'fan', 'FAN11G3290' => 'fan', 'FAN16G0937' => 'fan', 'FAN16G3388' => 'fan', 'FAN21G1108' => 'fan', 'FAN21G2873' => 'fan', 'FAN25G0332' => 'fan', 'FAN25G1246' => 'fan', 'FvH4_3g10000' => 'fve', 'FvH4_3g32040' => 'fve', 'Glyma.09G023200' => 'gma', 'Glyma.11G145600' => 'gma', 'Glyma.12G076100' => 'gma', 'Glyma.12G174000' => 'gma', 'Glyma.13G325400' => 'gma', 'Glyma.15G129300' => 'gma', 'Gohir.A03G033100' => 'ghi', 'Gohir.A05G103700' => 'ghi', 'Gohir.A05G110200' => 'ghi', 'Gohir.A08G198600' => 'ghi', 'Gohir.A10G003600' => 'ghi', 'Gohir.A13G230800' => 'ghi', 'Gohir.D03G135300' => 'ghi', 'Gohir.D04G022336' => 'ghi', 'Gohir.D04G058150' => 'ghi', 'Gohir.D05G103500' => 'ghi', 'Gohir.D05G110500' => 'ghi', 'Gohir.D05G308500' => 'ghi', 'Gohir.D08G216000' => 'ghi', 'Gohir.D10G003600' => 'ghi', 'Gohir.D11G231400' => 'ghi', 'Gohir.D13G236300' => 'ghi', 'Gohir.D13G236366' => 'ghi', 'Gorai.003G142400' => 'gra', 'Gorai.004G229800' => 'gra', 'Gorai.009G107700' => 'gra', 'Gorai.009G114900' => 'gra', 'Gorai.011G004000' => 'gra', 'Gorai.013G267000' => 'gra', 'GSVIVG01021620001' => 'vvi', 'GSVIVG01025195001' => 'vvi', 'HanXRQChr01g0019351' => 'han', 'HanXRQChr02g0055831' => 'han', 'HanXRQChr04g0119181' => 'han', 'HanXRQChr14g0452721' => 'han', 'HanXRQChr15g0480941' => 'han', 'HanXRQChr15g0480951' => 'han', 'Haze_05778' => 'cav', 'Haze_23815' => 'cav', 'Hma1.2p1_0125F.1_g059090' => 'hma', 'Hma1.2p1_0186F.1_g081730' => 'hma', 'Hma1.2p1_0208F.1_g088130' => 'hma', 'Hma1.2p1_0307F.1_g119750' => 'hma', 'Hma1.2p1_0333F.1_g128330' => 'hma', 'Hma1.2p1_0419F.1_g149400' => 'hma', 'Hma1.2p1_0536F.1_g174070' => 'hma', 'Hma1.2p1_0783F.1_g217015' => 'hma', 'Hma1.2p1_0946F.1_g240363' => 'hma', 'HPP92_005881' => 'vpl', 'HPP92_009348' => 'vpl', 'HPP92_009363' => 'vpl', 'HPP92_009386' => 'vpl', 'HPP92_009409' => 'vpl', 'HPP92_009446' => 'vpl', 'Hund08185' => 'sun', 'Hund17716' => 'sun', 'Lalb_Chr01g0004331' => 'lal', 'Lalb_Chr03g0027421' => 'lal', 'Lalb_Chr14g0374621' => 'lal', 'Lalb_Chr15g0088731' => 'lal', 'Lalb_Chr18g0057921' => 'lal', 'Lalb_Chr19g0137201' => 'lal', 'Lalb_Chr20g0120021' => 'lal', 'Lalb_Chr22g0350261' => 'lal', 'Lj1A1163G28' => 'lonja', 'Lj1A203G60' => 'lonja', 'Lj1A203T63' => 'lonja', 'Lj1C1163T10' => 'lonja', 'Lj1C205G6' => 'lonja', 'Lj2A329T52' => 'lonja', 'Lj2C1026G5' => 'lonja', 'Lj3g0016486' => 'lja', 'Lj3g0016619' => 'lja', 'Lj6g0011526' => 'lja', 'LjContig00408g0026738' => 'lja', 'Lsat_1_v5_gn_1_117821' => 'lsa', 'Lsat_1_v5_gn_1_64141' => 'lsa', 'Lsat_1_v5_gn_2_100160' => 'lsa', 'Lsat_1_v5_gn_7_29460' => 'lsa', 'Manes.04G019900' => 'mes', 'Manes.06G055400' => 'mes', 'Manes.06G055500' => 'mes', 'Manes.11G146300' => 'mes', 'Mapoly0001s0206' => 'mpo', 'MBI02_g20984_MAGBIO' => 'mbi', 'MBI02_g43298_MAGBIO' => 'mbi', 'MBI10_g21918_MAGBIO' => 'mbi', 'MBI18_g10582_MAGBIO' => 'mbi', 'MCO13G247' => 'mco', 'MD03G1119200' => 'mdo', 'MD05G1274100' => 'mdo', 'MD10G1253800' => 'mdo', 'MD11G1137000' => 'mdo', 'Medtr2g029960' => 'mtr', 'Medtr2g094550' => 'mtr', 'MELO3C007081.2' => 'cme', 'MELO3C025776.2' => 'cme', 'MELO3C029007.2' => 'cme', 'MELO3C029546.2' => 'cme', 'MELO3C029659.2' => 'cme', 'Migut.D02229' => 'egut', 'Migut.H01336' => 'egut', 'Migut.M01887' => 'egut', 'Migut.N02594' => 'egut', 'MSTRG.16287' => 'ama', 'MSTRG.17795' => 'ama', 'MSTRG.18665' => 'ama', 'MSTRG.7534' => 'ama', 'Nitab4.5_0000106g0190' => 'nta', 'Nitab4.5_0000181g0130' => 'nta', 'Nitab4.5_0000602g0140' => 'nta', 'Nitab4.5_0002719g0110' => 'nta', 'Nitab4.5_0003131g0010' => 'nta', 'Nitab4.5_0003747g0040' => 'nta', 'Nitab4.5_0004077g0030' => 'nta', 'Nitab4.5_0009422g0010' => 'nta', 'Nitab4.5_0016156g0010' => 'nta', 'Nn2g10808' => 'nnu', 'Nn2g13108' => 'nnu', 'Nn3g20238' => 'nnu', 'Oeu001278.1' => 'oeu', 'Oeu013464.1' => 'oeu', 'Oeu015184.3' => 'oeu', 'Oeu039504.2' => 'oeu', 'Oeu041099.1' => 'oeu', 'Oeu058476.1' => 'oeu', 'Oeu060304.2' => 'oeu', 'Os01g0585700' => 'osa', 'Os01g0586000' => 'osa', 'Os04g0620400' => 'osa', 'Os05g0592500' => 'osa', 'Peaxi162Scf00029g00127' => 'pax', 'Peaxi162Scf00270g00423' => 'pax', 'Peaxi162Scf00670g00344' => 'pax', 'PGR031G0352' => 'pgr', 'PGR102G2930' => 'pgr', 'PGR119G0314' => 'pgr', 'PGSC0003DMG400001898' => 'stu', 'PGSC0003DMG400005562' => 'stu', 'PGSC0003DMG400024322' => 'stu', 'PGSC0003DMG401008055' => 'stu', 'PGSC0003DMG402008055' => 'stu', 'Phvul.005G134600' => 'pvu', 'Phvul.006G129000' => 'pvu', 'Phvul.011G080000' => 'pvu', 'Potri.004G211500' => 'ptr', 'Potri.009G014700' => 'ptr', 'Pp3c12_11280' => 'ppa', 'Pp3c3_35620' => 'ppa', 'Pp3c4_5240' => 'ppa', 'Pp3c8_2730' => 'ppa', 'PRCOL_00003466' => 'pco', 'Prupe.4G089700' => 'ppe', 'Prupe.6G102600' => 'ppe', 'Psat1g168080' => 'psa', 'Psat5g280040' => 'psa', 'Psat7g225280' => 'psa', 'PSO063G0892' => 'pso', 'PSO339G5983' => 'pso', 'PSO339G6545' => 'pso', 'PSO384G4521' => 'pso', 'PSO541G0366' => 'pso', 'PSO675G2882' => 'pso', 'QL01p021969' => 'qlo', 'QL05p053069' => 'qlo', 'QL93p1903_0043' => 'qlo', 'QL93p1903_0072' => 'qlo', 'RcHm_v2.0_Chr5g0015881' => 'rch', 'RcHm_v2.0_Chr5g0049281' => 'rch', 'RcHm_v2.0_Chr5g0058771' => 'rch', 'Rhsim02G0160800' => 'rsi', 'Rhsim13G0094700' => 'rsi', 'Sabra04G0143000' => 'sbr', 'Sabra09G0007300' => 'sbr', 'SalBow3G3221' => 'sbo', 'SalBow3G4467' => 'sbo', 'SalBow7G2273' => 'sbo', 'Sc06g0010290' => 'sci', 'Sc06g0010300' => 'sci', 'Sc24g0001370' => 'sci', 'Sed0004512' => 'sed', 'Sed0009099' => 'sed', 'Sed0013009' => 'sed', 'Sed0017918' => 'sed', 'Sed0023225' => 'sed', 'SEGI_01487' => 'sgi', 'SEGI_05232' => 'sgi', 'SEGI_27652' => 'sgi', 'SEGI_32965' => 'sgi', 'SGA_v2.0_scaffold174G39204' => 'sas', 'SGA_v2.0_scaffold180G39670' => 'sas', 'SGA_v2.0_scaffold1G00239' => 'sas', 'SGA_v2.0_scaffold223G42859' => 'sas', 'SHI19580' => 'shi', 'SMO181G0023' => 'smo', 'SMO200G0196' => 'smo', 'SMO200G0207' => 'smo', 'Solyc02g069780.3' => 'sly', 'Solyc06g011665.1' => 'sly', 'Solyc06g075160.3' => 'sly', 'Solyc11g069490.3' => 'sly', 'Sopen02g018940' => 'spe', 'Sopen06g007430' => 'spe', 'Sopen06g031570' => 'spe', 'Sopen11g028200' => 'spe', 'Sp1g06630' => 'spa', 'Sp1g26290' => 'spa', 'Sp4g11150' => 'spa', 'Sp5g16130' => 'spa', 'TAR623G1606' => 'tar', 'TAR626G1145' => 'tar', 'TAR626G1905' => 'tar', 'TAR633G1112' => 'tar', 'TAR636G1054' => 'tar', 'THA.LOC104798604' => 'tha', 'THA.LOC104799507' => 'tha', 'THA.LOC104800601' => 'tha', 'THA.LOC104812685' => 'tha', 'THA.LOC104814323' => 'tha', 'THA.LOC104814826' => 'tha', 'THA.LOC104826368' => 'tha', 'Thecc.06G001000' => 'tca', 'Thecc.09G341800' => 'tca', 'Thhalv10002405m.g' => 'esa', 'Thhalv10006825m.g' => 'esa', 'Thhalv10006836m.g' => 'esa', 'Thhalv10016277m.g' => 'esa', 'TPR.G11521' => 'tpr', 'TPR.G17308' => 'tpr', 'TPR.G26362' => 'tpr', 'TPR.G31081' => 'tpr', 'TPR.G36385' => 'tpr', 'TWI09G0259' => 'twi', 'TWI31G0678' => 'twi', 'TWI53G1121' => 'twi', 'TWI79G0248' => 'twi', 'unitig_22.g6660' => 'ugi', 'unitig_749.g13810' => 'ugi', 'unitig_8.g3302' => 'ugi', 'vmacro03201' => 'vma', 'vmacro10972' => 'vma', 'VMungo0540G1261' => 'vmu', 'VMungo1080G1805' => 'vmu', 'VMungo1127G0686' => 'vmu', 'Zm00001eb070360' => 'zma', 'Zm00001eb160600' => 'zma', 'Zm00001eb297310' => 'zma', 'Zm00001eb357330' => 'zma', 'Zm00001eb431180' => 'zma' ) $gf_id = 'HOM05D001466' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001466' ) $data_identifier = 'HOM05D001466' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 21, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 17, 'bol' => (int) 10, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 1, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 6, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 2, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 6, 'cav' => (int) 2, 'hma' => (int) 9, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb431180' $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